The aim of this study was to explore the relationship of iron and zinc deficiencies and anemia in children aged under 5 years living in malaria endemic area of South Kivu/DRC. We conducted a cross-sectional study in the health zone of Miti Murhesa in South Kivu/DRC. A total of 1088 children in good general health were included in this study. Almost 40% of children were anemic. The prevalence of iron deficiency (ID) was found in 34.9% and 49.1% children based on ferritin or free erythrocyte protoporphyrin (FEP), respectively. If anemia is present, we found iron deficiency anemia (IDA) according to the WHOcriteria (ferritin) in 31%, and according to FEP in 66% of children. The overall prevalence of zinc deficiency was 17.6%. If anemia is present, zinc deficiency was found in 24.4% of children. Inflammation/infection, based upon CRP, was present in 39.7% children. The independent factors associated with anemia were recent illness, middle upper arm circumference, weight-for-height, ID according to FEP, zinc deficiency, and submicroscopic Plasmodium infection. A high prevalence of ID was observed in children in South Kivu according to FEP. Ferritin as acute phase protein was less suited in this population due to a high frequency of infection/inflammation. Iron and zinc deficiencies were found to be significantly associated with anemia in this population.